Isn't it true that cosmonauts were killed in suborbital flights before Gagarin? Or on orbital flights that later were covered up?

There does not seem to be any truth at all. All of these stories stem from various newspaper and magazine articles of the early sixties. The apogee of this trend was a pulp publication by Lloyd Nolan in 1966, The Soviet Space Hoax, which claimed that not only were there many deaths but that the entire Soviet space and missile programs were a hoax! Although the Soviets were certainly providing a lot of disinformation (the annulus counterweight on the Vostok with shroud when first shown suspended below a helicopter at Red Square, the Korolev GB-1 "SS-10/Scrag" 'Global Missile'), there is no evidence at all that they really occurred and they have been thoroughly debunked with all the information that came out since the collapse of the Soviet Union. The story of Ilyushin's son being injured in a spaceflight was actually debunked as long ago as 1967 - see Ken Gatland's Manned Spacecraft of that year. Jim Oberg's full account of the phantom cosmonaut myth is HERE.

Aside from everything else, it is clear that the Soviet Union did not have the resources to be pursuing a parallel 'more secret' manned program. As Roads to Space notes, Korolev ruled out any ballistic suborbital manned program, and all of the Vostok precursor flights are accounted for.

Of course, one must always keep an open mind ... for example, it appears that there was a pilot killed in a test of the Vostok ejection seat from a high altitude balloon, even though various Russian sources to this day give varying 'inside' accounts of the event.